If actually you don't develop a plug-in for MS Excel but rather a desktop application,then it is better to use ConvertFile method as previously.
Can you convert documents successfully when SkipEmptySheets is false? If so, what does not satisfy you in this case?

We tried but could not duplicate this problem in our testing environment even with your sample Excel file. During our testing your document was always converted successfully. Which version of MS Excel do you have?

“Before printing timeout" error means that Print2Flash successfully instructed an application (in your case MS Excel) to print the document but the application did not start printing within the time period specified by BeforePrintingTimeout parameter. Print2Flash waits until BeforePrintingTimeout expires and returns that error in this situation. Print2Flash in itself can do nothing about this situation as it is a virtual printer and it cannot convert a document unless an application sends a printing job to it. Please see this forum topic for more information: viewtopic.php?f=19&t=5&p=5

System.Runtime.InteropServices.COMException (0x800A03EC): Microsoft Office Excel cannot access the file 'D:\RadioSQA\NLR\WIP'. There are several possible reasons: • The file name or path does not exist. • The file is being used by another program. • The workbook you are trying to save has the same name as a currently open workbook.